Making a hole in an existing object

Hey! I have an STL I downloaded, and there’s a flat surface, aligned with the ground that I’d like to make some holes in. I can draw the shapes, but because the object is floating above/below the surface, any extrusion just adds material rather than subtracting it.

I suppose my question could be, how do I force an extrusion to be negative space rather than positive? I hope I’m describing this correctly.

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STL’s can be tricky to work with. Here, the orange body is an STL object. I extrude a cylinder thru the STL and then subtract it.

Thanks TigerMike! I played around some more yesterday after posting, and that’s the same solution I came up with. It got me where I wanted to go.

Here’s another tidbit. Sometimes I make the STL semi-transparent (temporarily) so I can see how much I want to create a recess when I don’t want it all the way thru the part.